Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate Pf6N2E2_1717 Anthranilate synthase, aminase component (EC 4.1.3.27)
Query= curated2:O66849 (494 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1717 Length = 489 Score = 263 bits (672), Expect = 1e-74 Identities = 154/367 (41%), Positives = 221/367 (60%), Gaps = 21/367 (5%) Query: 124 GYFAYDVVKFYEPVEDKNPDPIHTYDIYLVLTDVVVIHDNLTGKIKVVVPIFAQNGIEEE 183 GYF+YD V+ E + D TYD L+ V + F NGI E Sbjct: 132 GYFSYDCVRLIERLPDLAKQ---TYDYPLIALSVYQ-----------TLVYFHSNGIVET 177 Query: 184 YERAKNL-----IRDTVKKLKERGTTFLNVVEKEPDFKNWRSNFTKEEFEDIVKKAKEYI 238 +L + D + L + F+ R+ T E+F + V+ A E+I Sbjct: 178 LINNHDLWSPRTLEDYPFLSSTPASEALAPLPYPEGFEEERT-VTPEQFVERVEVAMEHI 236 Query: 239 AQGDVIQVVLSQRFRKRFKGNPDNIYRVLRFLNPSPYMYYLDFDQLKVIGSSPEILVRLE 298 GDV Q+ L R R + +P ++Y+ LR NPSPYMY + +IG+SPE+ VR++ Sbjct: 237 RAGDVYQIQLGHEIRIRSQVSPFDVYQNLRLRNPSPYMYLAHVGGIDLIGASPELFVRIK 296 Query: 299 EGRIETRPIAGTRKRGRTEEEDKRLEEDLLSDEKERAEHLMLVDLARNDIGRVAKTGSVR 358 + IE RPIAGT + + + +L +L EKERAEHLML+DL RNDIGRV + GS+ Sbjct: 297 DDLIEMRPIAGTVGK-KPGVDPTQLVLELTRSEKERAEHLMLIDLCRNDIGRVCQAGSLE 355 Query: 359 VENFMRIERYSHVMHIVSDVVGELREGYDALDVLKATFPAGTVSGAPKVRAMQIIEELEN 418 V+ FM +E YSH+ H+VS+V G LR G DA DV+KA+FPAGT+SGAPKVRAM++IE +E+ Sbjct: 356 VDEFMLVEEYSHLYHMVSNVRGLLRPGLDAFDVIKASFPAGTMSGAPKVRAMELIEGMES 415 Query: 419 ERRGIYAGSVGYISFQGNMDMAIAIRTAVYRDRDIFVQAGAGIVADSVPEKEWEETVNKA 478 RRGIYAG++G + F G+++ A+ IR+ V+ + ++A AG+VADSVPE EW+ET+ K Sbjct: 416 NRRGIYAGALGLVGFDGSVNTALCIRSTVFDEGTYHLRASAGVVADSVPELEWKETLYKM 475 Query: 479 KALMKAI 485 ++ +A+ Sbjct: 476 GSVYRAV 482 Lambda K H 0.318 0.138 0.390 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 527 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 494 Length of database: 489 Length adjustment: 34 Effective length of query: 460 Effective length of database: 455 Effective search space: 209300 Effective search space used: 209300 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory